Recombination and positive selection contribute to evolution of Listeria monocytogenes inIA

The surface molecule INA interacts with E-cadherin to promote invasion of Listeria monocytogenes into selected host cells. DNA sequencing of inIA for 40 L. monocytogenes isolates revealed 107 synonymous and 45 nonsynonymous substitutions. A frameshift mutation in a homopolymeric tract encoding part of the InIA signal peptide was identified in three lineage 11 isolates, which also showed reduced ability to invade human intestinal epithelial cells. Phylogenies showed clear separation of inIA sequences into lineages I and II. Thirteen inIA recombination events, predominantly involving lineage 11 strains as recipients (112 events), were detected and a number of amino acid residues were shown to be under positive selection. Four of the 45 nonsynonymous changes were found to be under positive selection with posterior probabilities >95 %. Mapping of polymorphic and positively selected amino acid sites on the partial crystal structure for InIA showed that the internalin surface of the leucine-rich repeat (LRR) region that faces the INA receptor E-cadherin does not include any polymorphic sites; all polymorphic and positively selected amino acids mapped to the outer face of the LRR region or to other INA regions. The data show that (i) inIA is highly polymorphic and evolution of inIA involved a considerable number of recombination events in lineage 11 isolates; (ii) positive selection at specific amino acid sites appears to contribute to evolution of inIA, including fixation of recombinant events; and (iii) single-nucleotide deletions in a lineage II-specific 3' homopolymeric tract in inIA lead to complete loss of InIA or to production of truncated InIA, which conveys reduced invasiveness. In conclusion, inIA has a complex evolutionary history, which is consistent with L. monocytogenes' natural history as an environmental pathogen with broad host-range, including its adaptation to environments and hosts where different inIA alleles may provide a selective advantage or where inIA may not be required.